kheal/particulate_as_data_analysis

Repo for analyzing data for particulate arsenic work

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This github repository is the data analysis portion associated with the manuscript by Heal et. al "Diverse arsenic-containing lipids in the surface ocean", published in Limnology and Oceanography, DOI: 10.1002/lol2.10216.

Control.Rmd

The Control.Rmd file is the data analysis notebook, which creates arsenoliplid database, cleans ICPMS and QE data for further analysis, and calculates bulk and individual arsenic concentrations.

• Sources scripts from 'SourceCode' folder
• Sources files from 'MetaData' and 'RawOutput' folders
• Writes products into the 'Intermediates' folder

Exploration.Rmd

The Exploration.Rmd file is the data exploration notebook, which uses the arsenolipid databsae and ESI data to search for possibile matches in MS1 and MS2 space for arsenolipids. After these explorations, I manually inspected the output and curated a list of compounds saved in 'MetaData/Targeted_visually_IDd_2.csv'

• Sources scripts from 'SourceCode' folder
• Sources files from 'MetaData' and 'RawOutput' folders
• Writes products into the 'Intermediates' folder

Figures.Rmd

The Figures.Rmd file is the figure creation notebook. Main text and supplemental figures are both made and not separated in the output.

• Sources scripts from 'Figures/Code' folder
• Sources files from 'Intermediates'
• Writes products figures into the 'Figures/Manuscript_figures'

Tables.Rmd

The Tables.Rmd is the table creation notebook. Tables are made into csv tables and supplemental tables are combined into a .xcel file.

• Sources scripts from 'Tables/Code' folder
• Sources files from 'Intermediates' folder
• Writes products figures into the 'Manuscript_tables' and 'Manuscript_tables/SuppTables' folders